The overall thrust of this research initiative is to develop new and improved means for the structural characterization of polypeptide ions, including those formed from peptides derived from enzymatic or chemical digestion, whole proteins, and protein complexes. The near-term objective is to develop a new direction in tandem mass spectrometry that will enable a wide range of novel strategies to deal with protein identification/characterization problems. The vast majority of tandem mass spectrometry experiments rely on fragmentation as the key structurally informative reaction. In this work, we seek to add the capability for selective covalent or non-covalent derivatization of gaseous ions within the context of an MSn experiment. The development of specific gas-phase chemistries fundamentally enables the development of a very wide range of applications. Just as bio-conjugation chemistries in solution have become broadly used by the molecular biology research community in a wide range of measurement strategies, the ability to effect gas-phase bio- conjugation will enable many novel approaches to structural characterization. Among the interesting features of the gas-phase approach are that it is fast (i.e., tens of milliseconds time scale) and it completely avoids sample manipulation issues. The work will involve the development of novel selective reactions, many of which will be inspired by the rich bio-conjugation literature, the development of peptide ion-based applications, and the development of whole protein/protein complex ion-based applications, as reflected in the specific aims: Specific Aim 1: Discover/develop functional group specific ion/ion reactions for reactive amino acid side chains, including, but not limited to, lysine (and N-termini), residues with acidic side-chains (i.e., glutamic and aspartic acids) and C-termini, arginine, and cysteine, as well as common post-translational modifications, such as phosphate and sulfate. Specific Aim 2: Develop applications for the use of selective ion/ion reactions in the MSn of peptide ions in support of peptide-based (i.e., bottom-up) approaches in protein identification/characterization. Specific Aim 3: Develop applications for the use of selective ion/ion reactions in the MSn of intact protein and protein complex ions in support of protein-based (i.e., top-down) approaches in protein identification/characterization. The development of novel chemistries and methodologies based on selective gas-phase reactions will be relevant to many areas of bio-medical research by virtue of the role that tandem mass spectrometry already plays across the spectrum of health related science. The work in this proposal must necessarily be focused, and will be directed to protein analysis. However, functional group-specific gas-phase reactions can also lead to new applications in other areas, such as metabolomics, glycomics, lipidomics, etc. The potential bio- medical impact for this work, therefore, is unusually broad.